alexr wrote:If I start an import using the above mentioned commands using the bulk.yaml files and the filelist.tsv. Is is possible that the importer gets stuck and if so how can I check for that.
If you have the JDK installed, then `jps` should list all the Java processes running on the system. You can either use `jstack` to list what that process is doing or if you don't have that installed, `kill -QUIT` with the process ID will print out a stack trace to stdout that you can send us.
During testing I imported successfully >10 folders with small samples of images. Then I tried to import a large Volocity (Perkin Elmer) library. These libraries give me sometimes trouble, also when I import them using the insight client.
The Dataset of the Volocity Import shows in the Omero web and insight client, but no previews are displayed. When I try to open these I get a message displayed that the preview needs to be calculated.
Then after a long time the preview is visible.
It certainly sounds possible that this particular import could take a while.
Is it possible that during this time new imports are started using the bulk/filelist method? Or is the server busy during this time and this is not possible. Because I realised that during this time me and other users do not get the normal stdout from the import command.
Hmmm.... I'm a bit unclear on what's going on. Can you show us examples of what you're seeing?
Is there a way to check the activities on the OMERO server that are currently running?
`bin/omero sessions who` will show you who is logged in. Otherwise, you can use `jstack` with the server's pid.
alexr wrote:I checked the Managed Repositories on the OMERO Server. After the Volocity file was imported all other imports seam to have failed. I get the entries for the time stampes such as:
/OMERO/ManagedRepository/Alex R_3/2018-06/26/14-57-13.868
but instead of having the soft link in there it is empty. The same applies for all users.
I have upploaded the latest log life in the ManagedRepository since I hope you can get some clue from this.
The log doesn't show much other than that it's a sizeable import. Can you send the server log as well?
Are there any possible locks?
Not that I can think of.
~Josh